Dear Amber list experts,
I have MD simulated in Amber14 complex of enzyme with non covalent inhibitor.
The simulation was conducted in octahedral periodic cell with explicit water molecules
and counter ions.
I used a standard command for the analysis of total energy of the whole system along
the productive MD trajectory (summary.ETOT):
cd analysis_md3-md8
nohup perl $AMBERHOME/AmberTools/src/etc/process_mdout.perl ../5_/md3.out ../6_/md4.out ../7_/md5.out ../8_/md6.out ../9_/md7.out ../10_/md8.out &
My question is: How should I modify the command in order to calculate the summary.ETOT
of protein + ligand complex and also separately summary.ETOT (enzyme) and
summary.ETOT (ligand) only, without energy contribution of water and counter ions?
Thank you,
Michael
*****************************
Michael Shokhen, PhD
Associate Professor
Department of Chemistry
Bar Ilan University,
Ramat Gan, 52900
Israel
email: shokhen.mail.biu.ac.il<https://webmail.biu.ac.il/owa/redir.aspx?C=a160ef9b9a6b4d06992402715d3ee465&URL=mailto%3ashokhen%40mail.biu.ac.il>
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Received on Sun Feb 14 2016 - 02:00:03 PST
